Identification of a novel SARS-CoV-2 variant with a truncated protein in ORF8 gene by next generation sequencing
© 2022. The Author(s)..
Using next generation sequencing technology, we identified a novel SARS-CoV-2 variant with a truncated ORF8 protein mutation near the end of the viral genome from nucleotides 27,878 to 27,958. This point mutation from C to T at nucleotide 27,956 changed the amino acid codon CAA (glutamine) to a stop codon, TAA, created a novel stop codon in ORF8 gene, resulting in a much smaller ORF8 protein (26 aa) than the wild type ORF8 protein (121 aa). This variant belongs to Pango lineage B.1.1291, which also contains the D614G mutation in the Spike (S) gene. The B.1.1291 lineage is predominantly circulated in the United States of America (97.18%), although it was also found in other counties (Russia, Canada, Latvia, Chile, India, Japan, Colombia, Germany, Greece, Mexico, and UK). A total of 340 closely related variants to this novel variant were identified in GISAID database with collection dates ranged from 3/6/2020 to 10/21/2020. In addition, a search within NCBI Genbank database found that 108,405 of 873,230 (12.4%) SAR-CoV-2 complete genomes contain this truncated ORF8 protein mutation, indicating this mutation may arise spontaneously in other lineages as well. The wide distribution of this mutation indicates that this truncated ORF8 protein mutation may provide the virus a growth advantage and adaptive evolution.
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| Medienart: |
E-Artikel |
| Erscheinungsjahr: |
2022 |
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| Erschienen: |
2022 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:12 |
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| Enthalten in: |
Scientific reports - 12(2022), 1 vom: 17. März, Seite 4631 |
| Sprache: |
Englisch |
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| Beteiligte Personen: |
DeRonde, Stephanie [VerfasserIn] |
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| Links: |
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| Themen: |
Journal Article |
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| Anmerkungen: |
Date Completed 04.04.2022 Date Revised 03.11.2022 published: Electronic UpdateOf: Res Sq. 2021 Apr 21;:. - PMID 34013248 Citation Status MEDLINE |
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| doi: |
10.1038/s41598-022-08780-2 |
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| Förderinstitution / Projekttitel: |
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| PPN (Katalog-ID): |
NLM338320385 |
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| 100 | 1 | |a DeRonde, Stephanie |e verfasserin |4 aut | |
| 245 | 1 | 0 | |a Identification of a novel SARS-CoV-2 variant with a truncated protein in ORF8 gene by next generation sequencing |
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| 500 | |a published: Electronic | ||
| 500 | |a UpdateOf: Res Sq. 2021 Apr 21;:. - PMID 34013248 | ||
| 500 | |a Citation Status MEDLINE | ||
| 520 | |a © 2022. The Author(s). | ||
| 520 | |a Using next generation sequencing technology, we identified a novel SARS-CoV-2 variant with a truncated ORF8 protein mutation near the end of the viral genome from nucleotides 27,878 to 27,958. This point mutation from C to T at nucleotide 27,956 changed the amino acid codon CAA (glutamine) to a stop codon, TAA, created a novel stop codon in ORF8 gene, resulting in a much smaller ORF8 protein (26 aa) than the wild type ORF8 protein (121 aa). This variant belongs to Pango lineage B.1.1291, which also contains the D614G mutation in the Spike (S) gene. The B.1.1291 lineage is predominantly circulated in the United States of America (97.18%), although it was also found in other counties (Russia, Canada, Latvia, Chile, India, Japan, Colombia, Germany, Greece, Mexico, and UK). A total of 340 closely related variants to this novel variant were identified in GISAID database with collection dates ranged from 3/6/2020 to 10/21/2020. In addition, a search within NCBI Genbank database found that 108,405 of 873,230 (12.4%) SAR-CoV-2 complete genomes contain this truncated ORF8 protein mutation, indicating this mutation may arise spontaneously in other lineages as well. The wide distribution of this mutation indicates that this truncated ORF8 protein mutation may provide the virus a growth advantage and adaptive evolution | ||
| 650 | 4 | |a Journal Article | |
| 650 | 4 | |a Research Support, N.I.H., Extramural | |
| 650 | 4 | |a Research Support, Non-U.S. Gov't | |
| 650 | 4 | |a Research Support, U.S. Gov't, P.H.S. | |
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| 700 | 1 | |a Deuling, Hannah |e verfasserin |4 aut | |
| 700 | 1 | |a Parker, Jayme |e verfasserin |4 aut | |
| 700 | 1 | |a Chen, Jack |e verfasserin |4 aut | |
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